-------after setenv FREESURFER_HOME and source command-------
chiaming-PORTEGE-R835:~> setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/Dickey-Pilot/003
chiaming-PORTEGE-R835:~> recon-all -i $SUBJECTS_DIR/003-0001-00003-0.dcm -s mike-dickey -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/003
Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer
Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
mri_motion_correct.fsl: Command not found.
talairach_avi: Command not found.
tkregister2_cmdl: Command not found.
nu_correct: Command not found.
mri_make_uchar: Command not found.
mri_normalize: Command not found.
mri_watershed: Command not found.
mri_gcut: Command not found.
mri_segment: Command not found.
mri_label2label: Command not found.
mri_em_register: Command not found.
mri_ca_normalize: Command not found.
mri_ca_register: Command not found.
mri_ca_label: Command not found.
mri_pretess: Command not found.
mri_fill: Command not found.
mri_tessellate: Command not found.
mri_concatenate_lta: Command not found.
mri_normalize_tp2: Command not found.
mris_smooth: Command not found.
mris_inflate: Command not found.
mris_curvature: Command not found.
mris_sphere: Command not found.
mris_fix_topology: Command not found.
mris_topo_fixer: Command not found.
mris_ca_label: Command not found.
mris_euler_number: Command not found.
mris_make_surfaces: Command not found.
mris_register: Command not found.
mris_volmask: Command not found.
mris_anatomical_stats: Command not found.
mrisp_paint: Command not found.
mris_curvature_stats: Command not found.
mris_calc: Command not found.
mri_robust_register: Command not found.
mri_robust_template: Command not found.
mri_and: Command not found.
mri_or: Command not found.
mri_fuse_segmentations: Command not found.
mri_segstats: Command not found.
cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or directory
/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/003/mike-dickey

 mri_convert /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/003/003-0001-00003-0.dcm /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/003/mike-dickey/mri/orig/001.mgz 

mri_convert: Command not found.
Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s mike-dickey exited with ERRORS at Sun Sep  7 20:35:50 EDT 2014

For more details, see the log file /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/003/mike-dickey/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting